HEADER DE NOVO PROTEIN 26-APR-26 13AG TITLE HELLOB-GGSSTSAA-A6DPP-ATP - DE NOVO PEPTIDE WITH TERTIARY STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HELLOB-GGSSTSAA-A6DPP+ATP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS SYNTHETIC CONSTRUCT, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.GANATRA REVDAT 1 28-OCT-26 13AG 0 JRNL AUTH P.GANATRA,D.F.WANG,S.NICHOLS,V.T.DANG,J.S.BRUNZELLE,P.JANA, JRNL AUTH 2 A.I.NGUYEN JRNL TITL POROUS FRAMEWORK ASSEMBLY CREATES FUNCTIONAL TERTIARY FOLDS JRNL TITL 2 IN SMALL PEPTIDES JRNL REF J.AM.CHEM.SOC. 2026 JRNL REFN ESSN 1520-5126 REMARK 2 REMARK 2 RESOLUTION. 0.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 9444 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1722 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 15.6100 - 2.1500 0.99 1310 141 0.1052 0.1520 REMARK 3 2 2.1500 - 1.7100 0.99 1320 142 0.1138 0.1134 REMARK 3 3 1.7100 - 1.4900 0.99 1272 139 0.1197 0.1252 REMARK 3 4 1.4900 - 1.3600 1.00 1330 148 0.1292 0.1301 REMARK 3 5 1.3600 - 1.2600 0.98 1319 144 0.1294 0.1445 REMARK 3 6 1.2600 - 1.1800 0.97 1265 141 0.1381 0.1725 REMARK 3 7 1.1800 - 1.1300 0.97 1272 144 0.1420 0.1712 REMARK 3 8 1.1200 - 1.0800 0.99 1329 140 0.1559 0.1764 REMARK 3 9 1.0800 - 1.0300 0.99 1279 145 0.2100 0.2632 REMARK 3 10 1.0300 - 1.0000 0.97 1315 151 0.2361 0.2544 REMARK 3 11 1.0000 - 0.9700 0.99 1292 146 0.2899 0.3062 REMARK 3 12 0.9700 - 0.9400 0.98 1294 141 0.3156 0.3614 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.208 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 217 REMARK 3 ANGLE : 1.735 310 REMARK 3 CHIRALITY : 0.117 24 REMARK 3 PLANARITY : 0.004 32 REMARK 3 DIHEDRAL : 27.608 35 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 13AG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-26. REMARK 100 THE DEPOSITION ID IS D_1000307267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.670181 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9444 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.940 REMARK 200 RESOLUTION RANGE LOW (A) : 15.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ACETONITRILE, WATER, SLOW COOLING, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 18.93800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 4.59350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 18.93800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 4.59350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2B ATP A 101 O HOH A 201 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 221 DISTANCE = 6.13 ANGSTROMS DBREF 13AG A 1 21 PDB 13AG 13AG 1 21 SEQRES 1 A 21 Z7Z ALA AIB LEU AIB DPP AIB LEU AIB GLN AIB LEU GLY SEQRES 2 A 21 GLY SER SER THR SER ALA ALA NH2 HET Z7Z A 1 69 HET AIB A 3 13 HET AIB A 5 13 HET DPP A 6 12 HET AIB A 7 13 HET AIB A 9 13 HET AIB A 11 13 HET NH2 A 21 3 HET ATP A 101 43 HETNAM Z7Z BIPHENYL-4-CARBOXYLIC ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM DPP DIAMINOPROPANOIC ACID HETNAM NH2 AMINO GROUP HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 1 Z7Z C13 H10 O2 FORMUL 1 AIB 5(C4 H9 N O2) FORMUL 1 DPP C3 H8 N2 O2 FORMUL 1 NH2 H2 N FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 HOH *21(H2 O) HELIX 1 AA1 ALA A 2 LEU A 12 1 11 LINK C1 AZ7Z A 1 N ALA A 2 1555 1555 1.43 LINK C1 BZ7Z A 1 N ALA A 2 1555 1555 1.43 LINK C1 CZ7Z A 1 N ALA A 2 1555 1555 1.43 LINK C ALA A 2 N AIB A 3 1555 1555 1.33 LINK C AIB A 3 N ALEU A 4 1555 1555 1.33 LINK C AIB A 3 N BLEU A 4 1555 1555 1.32 LINK C ALEU A 4 N AIB A 5 1555 1555 1.33 LINK C BLEU A 4 N AIB A 5 1555 1555 1.33 LINK C AIB A 5 N DPP A 6 1555 1555 1.33 LINK C DPP A 6 N AIB A 7 1555 1555 1.33 LINK C AIB A 7 N ALEU A 8 1555 1555 1.32 LINK C AIB A 7 N BLEU A 8 1555 1555 1.33 LINK C ALEU A 8 N AIB A 9 1555 1555 1.33 LINK C BLEU A 8 N AIB A 9 1555 1555 1.33 LINK C AIB A 9 N GLN A 10 1555 1555 1.33 LINK C GLN A 10 N AIB A 11 1555 1555 1.32 LINK C AIB A 11 N LEU A 12 1555 1555 1.33 LINK C ALA A 20 N NH2 A 21 1555 1555 1.42 CRYST1 37.876 9.187 41.025 90.00 102.15 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.026402 0.000000 0.005684 0.00000 SCALE2 0.000000 0.108849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024934 0.00000 CONECT 1 4 CONECT 2 5 CONECT 3 6 CONECT 4 1 7 70 CONECT 5 2 8 70 CONECT 6 3 9 70 CONECT 7 4 10 16 CONECT 8 5 11 17 CONECT 9 6 12 18 CONECT 10 7 13 43 CONECT 11 8 14 44 CONECT 12 9 15 45 CONECT 13 10 22 46 CONECT 14 11 23 47 CONECT 15 12 24 48 CONECT 16 7 19 49 CONECT 17 8 20 50 CONECT 18 9 21 51 CONECT 19 16 22 52 CONECT 20 17 23 53 CONECT 21 18 24 54 CONECT 22 13 19 25 CONECT 23 14 20 26 CONECT 24 15 21 27 CONECT 25 22 28 31 CONECT 26 23 29 32 CONECT 27 24 30 33 CONECT 28 25 34 55 CONECT 29 26 35 56 CONECT 30 27 36 57 CONECT 31 25 37 58 CONECT 32 26 38 59 CONECT 33 27 39 60 CONECT 34 28 40 61 CONECT 35 29 41 62 CONECT 36 30 42 63 CONECT 37 31 40 64 CONECT 38 32 41 65 CONECT 39 33 42 66 CONECT 40 34 37 67 CONECT 41 35 38 68 CONECT 42 36 39 69 CONECT 43 10 CONECT 44 11 CONECT 45 12 CONECT 46 13 CONECT 47 14 CONECT 48 15 CONECT 49 16 CONECT 50 17 CONECT 51 18 CONECT 52 19 CONECT 53 20 CONECT 54 21 CONECT 55 28 CONECT 56 29 CONECT 57 30 CONECT 58 31 CONECT 59 32 CONECT 60 33 CONECT 61 34 CONECT 62 35 CONECT 63 36 CONECT 64 37 CONECT 65 38 CONECT 66 39 CONECT 67 40 CONECT 68 41 CONECT 69 42 CONECT 70 4 5 6 CONECT 72 80 CONECT 80 72 81 86 CONECT 81 80 82 84 85 CONECT 82 81 83 93 94 CONECT 83 82 CONECT 84 81 87 88 89 CONECT 85 81 90 91 92 CONECT 86 80 CONECT 87 84 CONECT 88 84 CONECT 89 84 CONECT 90 85 CONECT 91 85 CONECT 92 85 CONECT 93 82 CONECT 94 82 CONECT 97 131 CONECT 98 131 CONECT 131 97 98 132 137 CONECT 132 131 133 135 136 CONECT 133 132 134 144 CONECT 134 133 CONECT 135 132 138 139 140 CONECT 136 132 141 142 143 CONECT 137 131 CONECT 138 135 CONECT 139 135 CONECT 140 135 CONECT 141 136 CONECT 142 136 CONECT 143 136 CONECT 144 133 145 150 CONECT 145 144 146 148 151 CONECT 146 145 147 156 CONECT 147 146 CONECT 148 145 149 152 153 CONECT 149 148 154 155 CONECT 150 144 CONECT 151 145 CONECT 152 148 CONECT 153 148 CONECT 154 149 CONECT 155 149 CONECT 156 146 157 162 CONECT 157 156 158 160 161 CONECT 158 157 159 169 170 CONECT 159 158 CONECT 160 157 163 164 165 CONECT 161 157 166 167 168 CONECT 162 156 CONECT 163 160 CONECT 164 160 CONECT 165 160 CONECT 166 161 CONECT 167 161 CONECT 168 161 CONECT 169 158 CONECT 170 158 CONECT 173 207 CONECT 174 207 CONECT 207 173 174 208 213 CONECT 208 207 209 211 212 CONECT 209 208 210 220 CONECT 210 209 CONECT 211 208 214 215 216 CONECT 212 208 217 218 219 CONECT 213 207 CONECT 214 211 CONECT 215 211 CONECT 216 211 CONECT 217 212 CONECT 218 212 CONECT 219 212 CONECT 220 209 CONECT 222 237 CONECT 237 222 238 243 CONECT 238 237 239 241 242 CONECT 239 238 240 250 CONECT 240 239 CONECT 241 238 244 245 246 CONECT 242 238 247 248 249 CONECT 243 237 CONECT 244 241 CONECT 245 241 CONECT 246 241 CONECT 247 242 CONECT 248 242 CONECT 249 242 CONECT 250 239 CONECT 349 357 CONECT 357 349 358 359 CONECT 358 357 CONECT 359 357 CONECT 361 362 363 364 368 CONECT 362 361 CONECT 363 361 CONECT 364 361 CONECT 365 366 367 368 372 CONECT 366 365 CONECT 367 365 CONECT 368 361 365 CONECT 369 370 371 372 373 CONECT 370 369 CONECT 371 369 CONECT 372 365 369 CONECT 373 369 374 CONECT 374 373 375 392 393 CONECT 375 374 376 377 394 CONECT 376 375 381 CONECT 377 375 378 379 395 CONECT 378 377 396 CONECT 379 377 380 381 397 CONECT 380 379 398 CONECT 381 376 379 382 399 CONECT 382 381 383 391 CONECT 383 382 384 400 CONECT 384 383 385 CONECT 385 384 386 391 CONECT 386 385 387 388 CONECT 387 386 401 402 CONECT 388 386 389 CONECT 389 388 390 403 CONECT 390 389 391 CONECT 391 382 385 390 CONECT 392 374 CONECT 393 374 CONECT 394 375 CONECT 395 377 CONECT 396 378 CONECT 397 379 CONECT 398 380 CONECT 399 381 CONECT 400 383 CONECT 401 387 CONECT 402 387 CONECT 403 389 MASTER 221 0 9 1 0 0 0 6 184 1 206 2 END